Research:Ions
Zinc
literature
Modeling of Zinc is one of our focuses so we need better understanding of the zinc-protein interactions.
I have collect some papers in /opt/reprints/ion-proteins/ZN-pro and …/ZN-MMP
In Zn-pro:
The zinc-finger.pdf has discussion of various CCCC, CCHC, CCHH complexation with Zn. It suggests that two of the C (cys) lose protons and the total charge of the Zn[CCCC] would be 0.
However zn-cystine-expt-solv-lim.pdf suggests that all 4 Cys should lose their protons, since their calculations seem to reproduce the crystal coordination structure.
Gresh has a review in zn-gresh-review.pdf and Carmay lim also has a review in zn-lim-rev.pdf.
The Zn-MMP/amy-mmps/ directory has all the MMP papers from Amy Song at FSU.
We should all read these and other papers in these two directories. Besides, protein simulations, we need some simple test cases (e.g. to compare with QM) to verify our model.
Zn++ and small ligands
/opt/reprints/ion-proteins/ZN-pro/zn-gresh*
especially the review
Prasad, R. N., Agrawal, M., and George, R. (2005) Mixed ligand complexes of nickel-, copper- and zinc(II) with 5-chloro(orbromo)salicylaldehyde and hydroxyaromatic aldehydes or ketones, J Indian Chem Soc 82, 445-447.
MMPs and Zinc modeling
Oscar presentation on Zinc model 
Previous Tetrahedron-Shaped Zinc molde
http://mayoresearch.mayo.edu/camdl/zinc_protein.cfm Here we can find examples to show our model is working
Mg
Mg++ chelating small molecules
A computational paper: New method to estimate stability of chelate complexes
http://arxiv.org/abs/0910.0357
More expt papers (found in the ref) below
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Mg++ Expt referecens:
1. Alegria, A. E., Garcia, C., Santiago, G., Collazo, G., and Morant, J. (2000) Intramolecular hydrogen bonding in hydroxylated semiquinones inhibits semiquinone-Mg2+ complex formation, J Chem Soc Perk T 2, 1569-1573.
2. Blindauer, C. A., Holy, A., and Sigel, H. (1999) Metal ion-binding properties of the nucleotide analogue 1-[2-(phosphonomethoxy)ethyl] cytosine (PMEC) in aqueous solution, Collect Czech Chem C 64, 613-632.
3. Doroshenko, A. O., Grigorovich, A. V., Posokhov, E. A., Pivovarenko, V. G., Demchenko, A. P., and Sheiko, A. D. (2001) Complex formation between azacrown derivatives of dibenzylidenecyclopentanone and alkali-earth metal ions, Russ Chem B+ 50, 404-412.
4. Gomez-Coca, R. B., Kapinos, L. E., Holy, A., Vilaplana, R. A., Gonzalez-Vilchez, F., and Sigel, H. (2000) Metal ion-binding properties of 9-(4-phosphonobutyl)adenine (dPMEA), a sister compound of the antiviral nucleotide analogue 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA), and quantification of the equilibria involving four Cu(PMEA) isomers, J Chem Soc Dalton, 2077-2084.
5. Kilyen, M., Lakatos, A., Latajka, R., Labadi, I., Salifoglou, A., Raptopoulou, C. P., Kozlowski, H., and Kiss, T. (2002) Al(III)-binding properties of iminodiacetic acid, nitrilotriacetic acid and their mixed carboxylic-phosphonic derivatives, J Chem Soc Dalton, 3578-3586.
6. Knobloch, B., Da Costa, C. P., Linert, W., and Sigel, H. (2003) Stability constants of metal ion complexes formed with N3-deprotonated uridine in aqueous solution, Inorg Chem Commun 6, 90-93.
7. Knobloch, B., Linert, W., and Sigel, H. (2005) Metal ion-binding properties of (N3)-deprotonated uridine, thymidine, and related pyrimidine nucleosides in aqueous solution, P Natl Acad Sci USA 102, 7459-7464.
8. Knobloch, B., Linert, W., and Sigel, H. (2005) Metal ion-binding properties of (N3)-deprotonated uridine, thymidine, and related pyrimidine nucleosides in aqueous solution, P Natl Acad Sci USA 102, 7459-7464.
9. Knobloch, B., and Sigel, H. (2004) A quantitative appraisal of the ambivalent metal ion binding properties of cytidine in aqueous solution and an estimation of the anti-syn energy barrier of cytidine derivatives, J Biol Inorg Chem 9, 365-373.
10. Prasad, R. N., and Agrawal, A. (2006) Synthesis and spectroscopic studies of mixed ligand complexes of cobalt(III) with salicylaldehyde, hydroxyaryl ketones and beta-diketones, J Indian Chem Soc 83, 75-77.
11. Prasad, R. N., Agrawal, A., and Sharma, K. M. (2006) Synthesis and spectral studies of mixed ligand complexes of cobalt(II) with carbonyl compounds, J Indian Chem Soc 83, 879-882.
12. Prasad, R. N., Agrawal, M., and George, R. (2003) Synthesis of mixed ligand complexes of nickel-, copper- and zinc(II) with 5-bromosalicylaldehyde and beta-diketones, J Indian Chem Soc 80, 79-81.
13. Prasad, R. N., Agrawal, M., and George, R. (2004) Mixed-ligand complexes of Ni(II), Cu(II), and Zn(II) with 5-chlorosalicylaldehyde and beta-diketones, Syn React Inorg Met 34, 943-952.
14. Prasad, R. N., Agrawal, M., and George, R. (2005) Mixed ligand complexes of nickel-, copper- and zinc(II) with 5-chloro(orbromo)salicylaldehyde and hydroxyaromatic aldehydes or ketones, J Indian Chem Soc 82, 445-447.
15. Prasad, R. N., Agrawal, M., and Malhotra, S. (2004) Ca(II) complexes of tetraazamacrocycles derived from 3,4-hexanedione and diaminoalkanes, J Serb Chem Soc 69, 661-668.
16. Prasad, R. N., Agrawal, M., Ratnani, R., and Saraswat, K. (2005) Mixed ligand complexes of alkaline earth metals. Part-XIV. Mg-II, Ca-II, Sr-II and Ba-II complexes with 5-nitrosalicylaldehyde and salicylaldehyde or hydroxyaromatic ketones, J Indian Chem Soc 82, 1003-1005.
17. Prasad, R. N., Agrawal, M., Ratnani, R., and Saraswat, K. (2005) Mixed ligand complexes of alkaline earth metals. Part-XIII. Mg-II, Ca-II, Sr-II and Ba-II complexes with 5-nitrosalicylaldehyde and beta-diketones, J Indian Chem Soc 82, 137-139.
18. Prasad, R. N., Agrawal, M., Ratnani, R., and Saraswat, K. (2006) Mixed ligand complexes of alkaline earth metals. Part-XV. Mg-II, Ca-II, Sr-II and Ba-II complexes with 2-hydroxy-1-naphthaldehyde and 2-hydroxybenzophenone, 5-bromosalicylaldehyde or 5-chlorosalicylaldehyde, J Indian Chem Soc 83, 957-960.
19. Prasad, R. N., Agrawal, M., and Sharma, M. (2002) Mixed ligand complexes of alkaline earth metals. Part-XI. Magnesium-, calcium-, strontium- and barium(II) complexes with 5-chlorosalicylaldehyde and beta-diketones, J Indian Chem Soc 79, 531-533.
20. Prasad, R. N., Agrawal, M., and Sharma, M. (2002) Mixed-ligand complexes of alkaline earth metals. IX. Mg(II), Ca(II), Sr(II), and Ba(II) complexes with 5-bromosalicylaldehyde and salicylaldehyde, 2-hydroxyacetophenone, or 2-hydroxypropiophenone, Syn React Inorg Met 32, 559-568.
21. Prasad, R. N., Agrawal, M., and Sharma, M. (2002) Mixed ligand complexes of alkaline earth metals: Part XII. Mg(II), Ca(II), Sr(H) and Ba(II) complexes with 5-chlorosalicylaldehyde and salicylaldehyde or hydroxyaromatic ketones, J Serb Chem Soc 67, 229-234.
22. Prasad, R. N., Agrawal, M., and Sharma, M. (2003) Mixed ligand complexes of alkaline earth metals. Part-X. Mg(II), Ca(II), Sr(II) and Ba(II) complexes with 5-bromosalicylaldehyde and -diketones, J Chil Chem Soc 48, 1-5.
23. Prasad, R. N., Agrawal, M., and Sharma, S. (2004) Copper(II) complexes of tetraazamacrocycles derived from beta-diketones and diaminoalkanes, Indian J Chem A 43, 337-340.
24. Prasad, R. N., Agrawal, M., and Sharma, S. (2005) Cobalt(II) complexes of tetraazamacrocycles derived from beta-diketones and diaminoalkanes, J Serb Chem Soc 70, 635-641.
25. Prasad, R. N., Sharma, K. M., and Agrawal, A. (2007) Synthesis and mass spectral studies of mixed ligand complexes of Co-II with 2-hydroxybenzophenone and beta-diketones, hydroxyaryl aldehydes or ketones, J Indian Chem Soc 84, 742-745.
26. Prasad, R. N., Sharma, K. M., and Agrawal, A. (2007) Mixed ligand complexes of Co(II) containing 5-bromosalicylaidehyde and beta-diketones, hydroxyaryl aldehydes or ketones, Indian J Chem A 46, 600-604.
27. Prasad, R. N., Sharma, K. M., and Agrawal, A. (2007) Synthesis and characterization of mixed ligand complexes of cobalt(II) with 2-hydroxy-1-naphthaldehyde and salicylaldehyde, hydroxyaromatic ketones or beta-diketonesn, J Indian Chem Soc 84, 34-36.
28. Roshal, A. D., Grigorovich, A. V., Doroshenko, A. O., Pivovarenko, V. G., and Demchenko, A. P. (1999) Flavonols as metal-ion chelators: complex formation with Mg2+ and Ba2+ cations in the excited state, J Photoch Photobio A 127, 89-100.
29. Sigel, H. (2004) Metal ion complexes of antivirally active nucleotide analogues. Conclusions regarding their biological action, Chem Soc Rev 33, 191-200.
30. Sigel, R. K. O., Sabat, M., Freisinger, E., Mower, A., and Lippert, B. (1999) Metal-modified base pairs involving different donor sites of purine nucleobases: trans-[a(2)Pt(7,9-DimeG-N1)(9-EtGH-N7)](2+) and trans-[a(2)Pt(7,9-DimeG-N1)(9-EtG-N7)](+) (a = NH3 or CH3NH2; 9-EtGH = 9-ethylguanine; 7,9-DimeG = 7,9-dimethylguanine). Possible relevance to metalated DNA triplex structures, Inorg Chem 38, 1481-1490.
31. Sodhi, J. S., Bryson, K., McGuffin, L. J., Ward, J. J., Wernisch, L., and Jones, D. T. (2004) Predicting metal-binding site residues in low-resolution structural models, J Mol Biol 342, 307-320.
32. Walker, N., Dobson, M. P., Wright, R. R., Barran, P. E., Murrell, J. N., and Stace, A. J. (2000) A gas-phase study of the coordination of Mg2+ with oxygen- and nitrogen-containing ligands, J Am Chem Soc 122, 11138-11145.